Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
Cebpb

Cell type

Cell type Class
Neural
Cell type
Microglia
MeSH Description
The third type of glial cell, along with astrocytes and oligodendrocytes (which together form the macroglia). Microglia vary in appearance depending on developmental stage, functional state, and anatomical location; subtype terms include ramified, perivascular, ameboid, resting, and activated. Microglia clearly are capable of phagocytosis and play an important role in a wide spectrum of neuropathologies. They have also been suggested to act in several other roles including in secretion (e.g., of cytokines and neural growth factors), in immunological processing (e.g., antigen presentation), and in central nervous system development and remodeling.

Attributes by original data submitter

Sample

source_name
Primary microglia
background
C57BL/6
age
P0-P2
genotype
Cop1 WT
cell type
Microglia
chip antibody
c/EBP<beta> (Santa Cruz H-7)

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Primary microglia were isolated from newborn mouse brains (P0-P2) as described (Lian et al., 2016). Briefly, hippocampi and cortices were mechanically dissociated and meninges removed with a 70 µm filter. Single cell suspensions from 4-5 brains were pooled in T-225 flasks (Corning) in Dulbecco's Modified Eagle Medium (DMEM) supplemented with 10% heat inactivated fetal bovine serum, 2 mM glutamine, 100 U/mL penicillin, and 100 μg/mL streptomycin (Gibco). The culture media was changed the next day to remove cell debris. After 10-14 days of culture, microglia were collected by shaking the flask at 110 rpm for 1 h. Microglia were plated on non-treated plates. The next day they were treated with 0.1 μM 4-hydroxytamoxifen (4-OHT, Sigma-Aldrich) for 48 h. Active Motif Epigenetic services performed ChIP assays. Cells fixed with 1% formaldehyde for 11 min were quenched with 0.25 M glycine and then were swollen in lysis buffer for 30 min on ice. Chromatin was isolated after sonication to shear the DNA to an average length of 300–500 bp. Input and immunoprecipitated DNAs were treated with RNase, proteinase K, and heat for de-crosslinking, followed by ethanol precipitation. Antibodies used for immunoprecipitation were c/EBPß (Santa Cruz H-7), H3K4me3 (Abcam ab8580) and H2K27ac (Abcam ab4729). Libraries were prepared using standard protocols for the Ovation Ultralow System. Briefly, samples were PCR-amplified and sized using the Agilent 2100Bioanalyzer. Barcoded libraries were sequenced 75 bp single end on HiSeq 2500 (Illumina).

Sequencing Platform

instrument_model
Illumina HiSeq 2500

mm10

Number of total reads
36429001
Reads aligned (%)
93.2
Duplicates removed (%)
36.5
Number of peaks
6748 (qval < 1E-05)

mm9

Number of total reads
36429001
Reads aligned (%)
93.1
Duplicates removed (%)
36.6
Number of peaks
6760 (qval < 1E-05)

Base call quality data from DBCLS SRA